A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
This report has been generated by the nf-core/quantms analysis pipeline. For information about how to interpret these results, please see the documentation.
Report
generated on 2022-07-28, 13:48
based on data in:
C:\Users\ASUS\Desktop\test_consensus_spectral_counting
pmultiqc
pmultiqc is a multiQC module to show the pipeline performance of mass spectrometry based quantification pipelines such as nf-core/quantms.
Experimental Design
This table shows the design of the experiment. I.e., which files and channels correspond to which sample/condition/fraction.
You can see details about it in https://abibuilder.informatik.uni-tuebingen.de/archive/openms/Documentation/release/latest/html/classOpenMS_1_1ExperimentalDesign.html
| Spectra File | Fraction_Group | Fraction | Label | Sample | MSstats_Condition | MSstats_BioReplicate |
|---|---|---|---|---|---|---|
| BSA1_F1.mzML | 1 | 1 | 1 | 1 | 1 | 1 |
| BSA1_F2.mzML | 1 | 2 | 1 | 1 | 1 | 1 |
| BSA2_F1.mzML | 2 | 1 | 1 | 2 | 2 | 2 |
| BSA2_F2.mzML | 2 | 2 | 1 | 2 | 2 | 2 |
| BSA3_F1.mzML | 3 | 1 | 1 | 3 | 3 | 3 |
| BSA3_F2.mzML | 3 | 2 | 1 | 3 | 3 | 3 |
HeatMap
This heatmap shows a performance overview of the pipeline
This plot shows the pipeline performance overview. Some metrics are calculated.
- Heatmap score[Contaminants]: as fraction of summed intensity with 0 = sample full of contaminants; 1 = no contaminants
- Heatmap score[Pep Intensity (>23.0)]: Linear scale of the median intensity reaching the threshold, i.e. reaching 2^21 of 2^23 gives score 0.25.
- Heatmap score[Charge]: Deviation of the charge 2 proportion from a representative Raw file (median). For typtic digests, peptides of charge 2 (one N-terminal and one at tryptic C-terminal R or K residue) should be dominant. Ionization issues (voltage?), in-source fragmentation, missed cleavages and buffer irregularities can cause a shift (see Bittremieux 2017, DOI: 10.1002/mas.21544 ).
- Heatmap score [MC]: the fraction (0% - 100%) of fully cleaved peptides per Raw file
- Heatmap score [MC Var]: each Raw file is scored for its deviation from the ‘average’ digestion state of the current study.
- Heatmap score [ID rate over RT]: Judge column occupancy over retention time. Ideally, the LC gradient is chosen such that the number of identifications (here, after FDR filtering) is uniform over time, to ensure consistent instrument duty cycles. Sharp peaks and uneven distribution of identifications over time indicate potential for LC gradient optimization.Scored using ‘Uniform’ scoring function. i.e. constant receives good score, extreme shapes are bad.
- Heatmap score [MS2 Oversampling]: The percentage of non-oversampled 3D-peaks. An oversampled 3D-peak is defined as a peak whose peptide ion (same sequence and same charge state) was identified by at least two distinct MS2 spectra in the same Raw file. For high complexity samples, oversampling of individual 3D-peaks automatically leads to undersampling or even omission of other 3D-peaks, reducing the number of identified peptides.
- Heatmap score [Pep Missing]: Linear scale of the fraction of missing peptides.
Summary Table
This table shows the quantms pipeline summary statistics
This table shows the quantms pipeline summary statistics
| #MS2 Spectra | #Identified MS2 Spectra | %Identified MS2 Spectra | #Peptides Identified | #Proteins Identified | #Proteins Quantified |
|---|---|---|---|---|---|
| 3136 | 153 | 4.88% | 51 | 21 | 20 |
Pipeline Result Statistics
This plot shows the quantms pipeline final result
This plot shows the quantms pipeline final result.
Including Sample Name、Possible Study Variables、identified the number of peptide in the pipeline、
and identified the number of modified peptide in the pipeline, eg. All data in this table are obtained
from the out_msstats file. You can also remove the decoy with the remove_decoy parameter.
| Spectra File | Sample Name | Condition | Fraction | #Peptide IDs | #Unambiguous Peptide IDs | #Modified Peptide IDs | #Protein (group) IDs |
|---|---|---|---|---|---|---|---|
| BSA1_F1.mzML | 1 | 1 | 1 | 18 | 17 | 9 | 7 |
| BSA1_F2.mzML | 1 | 1 | 2 | 13 | 13 | 4 | 5 |
| BSA2_F1.mzML | 2 | 2 | 1 | 15 | 14 | 8 | 5 |
| BSA2_F2.mzML | 2 | 2 | 2 | 15 | 15 | 5 | 4 |
| BSA3_F1.mzML | 3 | 3 | 1 | 22 | 21 | 11 | 9 |
| BSA3_F2.mzML | 3 | 3 | 2 | 9 | 9 | 3 | 4 |
Number of Peptides Per Protein
This plot shows the number of peptides per proteins in quantms pipeline final result
This statistic is extracted from the out_msstats file. Proteins supported by more peptide identifications can constitute more confident results.
Spectra Tracking
This plot shows the tracking of the number of spectra along the quantms pipeline
This table shows the changes in the number of spectra corresponding to each input file
during the pipeline operation. And the number of peptides finally identified and quantified is obtained from
the PSM table in the mzTab file. You can also remove decoys with the remove_decoy parameter.:
- MS1_Num: The number of MS1 spectra extracted from mzMLs
- MS2_Num: The number of MS2 spectra extracted from mzMLs
- MSGF: The Number of spectra identified by MSGF search engine
- Comet: The Number of spectra identified by Comet search engine
- PSMs from quant. peptides: extracted from PSM table in mzTab file
- Peptides quantified: extracted from PSM table in mzTab file
| Spectra File | #MS1 Spectra | #MS2 Spectra | MSGF | Comet | #PSMs from quant. peptides | #Peptides quantified |
|---|---|---|---|---|---|---|
| BSA1_F1.mzML | 286 | 481 | 209 | 174 | 34 | 18 |
| BSA1_F2.mzML | 278 | 639 | 298 | 275 | 27 | 13 |
| BSA2_F1.mzML | 257 | 557 | 219 | 211 | 18 | 15 |
| BSA2_F2.mzML | 267 | 609 | 251 | 229 | 28 | 15 |
| BSA3_F1.mzML | 290 | 383 | 159 | 146 | 30 | 21 |
| BSA3_F2.mzML | 298 | 467 | 195 | 167 | 16 | 9 |
Distribution of precursor charges
This is a bar chart representing the distribution of the precursor ion charges for a given whole experiment.
This information can be used to identify potential ionization problems including many 1+ charges from an ESI ionization source or an unexpected distribution of charges. MALDI experiments are expected to contain almost exclusively 1+ charged ions. An unexpected charge distribution may furthermore be caused by specific search engine parameter settings such as limiting the search to specific ion charges.
Number of Peaks per MS/MS spectrum
This chart represents a histogram containing the number of peaks per MS/MS spectrum in a given experiment. This chart assumes centroid data. Too few peaks can identify poor fragmentation or a detector fault, as opposed to a large number of peaks representing very noisy spectra. This chart is extensively dependent on the pre-processing steps performed to the spectra (centroiding, deconvolution, peak picking approach, etc).
Peak Intensity Distribution
This is a histogram representing the ion intensity vs. the frequency for all MS2 spectra in a whole given experiment. It is possible to filter the information for all, identified and unidentified spectra. This plot can give a general estimation of the noise level of the spectra.
Generally, one should expect to have a high number of low intensity noise peaks with a low number of high intensity signal peaks. A disproportionate number of high signal peaks may indicate heavy spectrum pre-filtering or potential experimental problems. In the case of data reuse this plot can be useful in identifying the requirement for pre-processing of the spectra prior to any downstream analysis. The quality of the identifications is not linked to this data as most search engines perform internal spectrum pre-processing before matching the spectra. Thus, the spectra reported are not necessarily pre-processed since the search engine may have applied the pre-processing step internally. This pre-processing is not necessarily reported in the experimental metadata.
Oversampling Distribution
An oversampled 3D-peak is defined as a peak whose peptide ion (same sequence and same charge state) was identified by at least two distinct MS2 spectra in the same Raw file.
For high complexity samples, oversampling of individual 3D-peaks automatically leads to undersampling or even omission of other 3D-peaks, reducing the number of identified peptides. Oversampling occurs in low-complexity samples or long LC gradients, as well as undersized dynamic exclusion windows for data independent acquisitions.
* Heatmap score [EVD: MS2 Oversampling]: The percentage of non-oversampled 3D-peaks.
Delta Mass
This chart represents the distribution of the relative frequency of experimental precursor ion mass (m/z) - theoretical precursor ion mass (m/z).
Mass deltas close to zero reflect more accurate identifications and also that the reporting of the amino acid modifications and charges have been done accurately. This plot can highlight systematic bias if not centered on zero. Other distributions can reflect modifications not being reported properly. Also it is easy to see the different between the target and the decoys identifications.
Summary of Search Engine
These plots contain search scores and PEPs counts for different search engines in different files, and they also contain a summary of the consensus PSMs if two or more search engines are used
This statistic is extracted from idXML files.
Summary of Search Scores
* SpecEvalue : Spectral E-values, the search score of MSGF. The value used for plotting is -lg(SpecEvalue).
* xcorr : cross-correlation scores, the search score of Comet. The value used for plotting is xcorr.
Summary of Posterior Error Probabilities
* PEP : Posterior Error Probability
Summary of consensus PSMs
Peptide Spectrum Matches
This plot shows the information of peptide spectrum matches
This table shows the information of peptide spectrum matches from mzTab PSM section.
| PSM_ID | Sequence | Accession | Search_Engine_Score | Spectra_Ref |
|---|---|---|---|---|
| 0 | DLGEEHFK | P02769|ALBU_BOVIN | 0.410 | BSA1_F1.mzML:spectrum=2779 |
| 1 | VYLASR | tr|A9FXS8|A9FXS8_SORC5 | 0.439 | BSA1_F1.mzML:spectrum=2610 |
| 2 | LVTDLTK | P02769|ALBU_BOVIN | 0.148 | BSA1_F1.mzML:spectrum=2861 |
| 3 | DLGEEHFK | P02769|ALBU_BOVIN | 0.059 | BSA1_F1.mzML:spectrum=2716 |
| 4 | LVEPSERR | tr|A9G7Q6|A9G7Q6_SORC5 | 0.551 | BSA1_F1.mzML:spectrum=2541 |
| 5 | YICDNQDTISSK | P02769|ALBU_BOVIN | 0.003 | BSA1_F1.mzML:spectrum=2791 |
| 6 | LCVLHEK | P02769|ALBU_BOVIN | 0.608 | BSA1_F1.mzML:spectrum=2841 |
| 7 | DLGEEHFK | P02769|ALBU_BOVIN | 0.414 | BSA1_F1.mzML:spectrum=2659 |
| 8 | LVTDLTK | P02769|ALBU_BOVIN | 0.018 | BSA1_F1.mzML:spectrum=2811 |
| 9 | ECCDKPLLEK | P02769|ALBU_BOVIN | 0.218 | BSA1_F1.mzML:spectrum=2625 |
| 10 | DDSPDLPK | P02769|ALBU_BOVIN | 0.271 | BSA1_F1.mzML:spectrum=2548 |
| 11 | CCTESLVNR | P02769|ALBU_BOVIN | 0.097 | BSA1_F1.mzML:spectrum=2609 |
| 12 | DLGEEHFK | P02769|ALBU_BOVIN | 0.133 | BSA1_F1.mzML:spectrum=2900 |
| 13 | ETYGDMADCCEK | P02769|ALBU_BOVIN | 0.014 | BSA1_F1.mzML:spectrum=2657 |
| 14 | MPALRTSR | tr|A9G573|A9G573_SORC5 | 0.568 | BSA1_F1.mzML:spectrum=2575 |
| 15 | CCTESLVNR | P02769|ALBU_BOVIN | 0.029 | BSA1_F1.mzML:spectrum=2566 |
| 16 | YICDNQDTISSK | P02769|ALBU_BOVIN | 0.285 | BSA1_F1.mzML:spectrum=2590 |
| 17 | DLGEEHFK | P02769|ALBU_BOVIN | 0.564 | BSA1_F1.mzML:spectrum=2837 |
| 18 | DLGEEHFK | P02769|ALBU_BOVIN | 0.047 | BSA1_F1.mzML:spectrum=2828 |
| 19 | LCVLHEK | P02769|ALBU_BOVIN | 0.139 | BSA1_F1.mzML:spectrum=2588 |
| 20 | DLGEEHFK | P02769|ALBU_BOVIN | 0.504 | BSA1_F1.mzML:spectrum=2663 |
| 21 | EYEATLEECCAK | P02769|ALBU_BOVIN | 0.171 | BSA1_F1.mzML:spectrum=2877 |
| 22 | MSVDSEVAER | tr|A9G6D0|A9G6D0_SORC5 | 0.376 | BSA1_F1.mzML:spectrum=2910 |
| 23 | CCTESLVNR | P02769|ALBU_BOVIN | 0.278 | BSA1_F1.mzML:spectrum=2633 |
| 24 | GSPAANVGVK | sp|O46375|TTHY_BOVIN | 0.260 | BSA1_F1.mzML:spectrum=2465 |
| 25 | YICDNQDTISSK | P02769|ALBU_BOVIN | 0.145 | BSA1_F1.mzML:spectrum=2547 |
| 26 | CPLMVK | sp|O46375|TTHY_BOVIN | 0.598 | BSA1_F1.mzML:spectrum=2494 |
| 27 | YICDNQDTISSK | P02769|ALBU_BOVIN | 0.066 | BSA1_F1.mzML:spectrum=2624 |
| 28 | AWSVAR | P02769|ALBU_BOVIN | 0.577 | BSA1_F1.mzML:spectrum=2730 |
| 29 | LCVLHEK | P02769|ALBU_BOVIN | 0.620 | BSA1_F1.mzML:spectrum=2880 |
| 30 | SHCIAEVEK | P02769|ALBU_BOVIN | 0.191 | BSA1_F1.mzML:spectrum=2458 |
| 31 | LSSPATLNSR | P00761|TRYP_PIGP06871|TRY1_CANFA | 0.185 | BSA1_F1.mzML:spectrum=2639 |
| 32 | DLGEEHFK | P02769|ALBU_BOVIN | 0.186 | BSA1_F1.mzML:spectrum=2769 |
| 33 | ECCDKPLLEK | P02769|ALBU_BOVIN | 0.173 | BSA1_F1.mzML:spectrum=2573 |
| 34 | HLVDEPQNLIK | P02769|ALBU_BOVIN | 0.219 | BSA1_F2.mzML:spectrum=3307 |
| 35 | AEFVEVTK | P02769|ALBU_BOVIN | 0.162 | BSA1_F2.mzML:spectrum=2993 |
| 36 | AGALLAAAGAR | tr|A9EN68|A9EN68_SORC5 | 0.526 | BSA1_F2.mzML:spectrum=3157 |
| 37 | DLGEEHFK | P02769|ALBU_BOVIN | 0.327 | BSA1_F2.mzML:spectrum=2976 |
| 38 | DDPHACYSTVFDK | P02769|ALBU_BOVIN | 0.470 | BSA1_F2.mzML:spectrum=3301 |
| 39 | HLVDEPQNLIK | P02769|ALBU_BOVIN | 0.303 | BSA1_F2.mzML:spectrum=3546 |
| 40 | VATVSLPR | P00761|TRYP_PIG | 0.441 | BSA1_F2.mzML:spectrum=3087 |
| 41 | VATVSLPR | P00761|TRYP_PIG | 0.339 | BSA1_F2.mzML:spectrum=3026 |
| 42 | DLGEEHFK | P02769|ALBU_BOVIN | 0.178 | BSA1_F2.mzML:spectrum=2946 |
| 43 | EAAVALLR | tr|A9EW37|A9EW37_SORC5 | 0.416 | BSA1_F2.mzML:spectrum=3227 |
| 44 | GACLLPK | P02769|ALBU_BOVIN | 0.159 | BSA1_F2.mzML:spectrum=2941 |
| 45 | SILDFVDR | tr|A9GP58|A9GP58_SORC5 | 0.348 | BSA1_F2.mzML:spectrum=3186 |
| 46 | YLYEIAR | P02769|ALBU_BOVIN | 0.067 | BSA1_F2.mzML:spectrum=3445 |
| 47 | EACFAVEGPK | P02769|ALBU_BOVIN | 0.050 | BSA1_F2.mzML:spectrum=3097 |
| 48 | HLVDEPQNLIK | P02769|ALBU_BOVIN | 0.104 | BSA1_F2.mzML:spectrum=3542 |
| 49 | EAAVALLR | tr|A9EW37|A9EW37_SORC5 | 0.273 | BSA1_F2.mzML:spectrum=3168 |
Protein Quantification Table
This plot shows the quantification information of proteins in the final result (mainly the mzTab file).
The quantification information (Spectral Counting) of proteins is obtained from the mzTab file. The table shows the quantitative level and distribution of proteins in different study variables and run.
- Peptides_Number: The number of peptides for each protein.
- Average Spectral Counting: Average spectral counting of each protein across all conditions with NA=0 or NA ignored.
- Spectral Counting in each condition (Eg.
CT=Mixture;CN=UPS1;QY=0.1fmol): Average spectral counting of replicates.
Click Show replicates to switch to bar plots of counting in each replicate.
| ProteinName | Peptides_Number | Average Spectrum Counting | 1 | 2 | 3 | 1 | 2 | 3 |
|---|---|---|---|---|---|---|---|---|
| sp|O46375|TTHY_BOVIN | 5 | 2 | 2 | 2 | 0 | |||
| P02769|ALBU_BOVIN | 27 | 40 | 44 | 35 | 0 | |||
| P00761|TRYP_PIG | 2 | 2 | 2 | 1 | 0 | |||
| tr|A9EW37|A9EW37_SORC5 | 1 | 2 | 2 | 0 | 0 | |||
| tr|A9GP58|A9GP58_SORC5 | 1 | 1 | 1 | 0 | 0 | |||
| tr|A9F9F1|A9F9F1_SORC5 | 1 | 1 | 1 | 0 | 0 | |||
| tr|A9G6D0|A9G6D0_SORC5 | 1 | 1 | 1 | 0 | 0 | |||
| tr|A9FXS8|A9FXS8_SORC5 | 1 | 1 | 1 | 0 | 0 | |||
| tr|A9EN68|A9EN68_SORC5 | 1 | 1 | 1 | 0 | 0 | |||
| tr|A9GKZ3|A9GKZ3_SORC5 | 1 | 1 | 1 | 0 | 0 | |||
| tr|A9G7Q6|A9G7Q6_SORC5 | 1 | 1 | 1 | 0 | 0 | |||
| tr|A9G573|A9G573_SORC5 | 1 | 1 | 1 | 0 | 0 | |||
| P46406|G3P_RABIT | 1 | 1 | 1 | 0 | 0 | |||
| tr|A9FKB2|A9FKB2_SORC5 | 1 | 1 | 0 | 1 | 0 | |||
| tr|A9GCS7|A9GCS7_SORC5 | 1 | 1 | 0 | 1 | 0 | |||
| tr|A9G7B7|A9G7B7_SORC5 | 1 | 1 | 0 | 1 | 0 | |||
| tr|A9FAQ3|A9FAQ3_SORC5 | 1 | 1 | 0 | 1 | 0 | |||
| tr|A9GCG3|A9GCG3_SORC5 | 1 | 1 | 0 | 1 | 0 | |||
| tr|A9F4M5|A9F4M5_SORC5 | 1 | 1 | 0 | 1 | 0 | |||
| tr|A9FTG3|A9FTG3_SORC5 | 1 | 1 | 0 | 1 | 0 |
nf-core/quantms Software Versions
are collected at run time from the software output.
| Process Name | Software | Version |
|---|---|---|
| CUSTOM_DUMPSOFTWAREVERSIONS | python | 3.9.5 |
| yaml | 5.4.1 | |
| FDRIDPEP | FalseDiscoveryRate | 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49 |
| IDFILTER | IDFilter | 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49 |
| IDPEP | IDPosteriorErrorProbability | 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49 |
| IDSCORESWITCHER | IDScoreSwitcher | 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49 |
| MZMLINDEXING | FileConverter | 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49 |
| PROTEOMICSLFQ | ProteomicsLFQ | 2.8.0-pre-exported-20220314 Mar 14 2022, 18:56:49 |
| SAMPLESHEET_CHECK | sdrf-pipelines | 0.0.21 |
| SEARCHENGINEMSGF | MSGFPlusAdapter | 2.8.0-pre-exported-20220227 Feb 27 2022, 20:31:47 |
| msgf_plus | MS-GF+ Release (v2021.03.22) (22 March 2021) | |
| Workflow | Nextflow | 21.10.6 |
| nf-core/quantms | 1.1dev |
nf-core/quantms Workflow Summary
- this information is collected when the pipeline is started.
Core Nextflow options
- runName
- hungry_linnaeus
- containerEngine
- docker
- launchDir
- /home/chengxin/newPR/quantms
- workDir
- /home/chengxin/newPR/quantms/work
- projectDir
- /home/chengxin/newPR/quantms
- userName
- chengxin
- profile
- test_lfq,docker
- configFiles
- /home/chengxin/newPR/quantms/nextflow.config
Input/output options
- input
- /home/chengxin/lfq_testdata/BSA_design_urls1.tsv
- outdir
- ./results_lfq
Protein database
- database
- /home/chengxin/lfq_testdata/18Protein_SoCe_Tr_detergents_trace_target_decoy.fasta
- decoy_string
- rev
Database search
- search_engines
- msgf
- instrument
- N/A
Modification localization
- luciphor_debug
- N/A
PSM re-scoring (general)
- posterior_probabilities
- fit_distributions
- run_fdr_cutoff
- 0.10
PSM re-scoring (Percolator)
- description_correct_features
- N/A
Consensus ID
- consensusid_considered_top_hits
- N/A
- min_consensus_support
- N/A
Isobaric analyzer
- select_activation
- HCD
Protein inference
- protein_level_fdr_cutoff
- 1.0
- psm_level_fdr_cutoff
- 1.0
Protein Quantification (DDA)
- labelling_type
- label free sample
- ratios
- N/A
- normalize
- N/A
- fix_peptides
- N/A
DIA-NN
- mass_acc_ms2
- 13
- mass_acc_ms1
- 7
- scan_window
- 8
Statistical post-processing
- contrasts
- pairwise
- add_triqler_output
- true
Quality control
- enable_pmultiqc
- true
Institutional config options
- config_profile_name
- Test profile for DDA LFQ
- config_profile_description
- Minimal test dataset to check pipeline function of the label-free quantification branch of the pipeline
Max job request options
- max_cpus
- 2
- max_memory
- 6 GB
- max_time
- 2d
Generic options
- hostnames
- N/A